Hi all,
I have the problem that there are a lot of files that are not deleted in the
database/files dir.
Among these files I have failed uploads and duplicated library files. The
latter do not correspond to new versions of existing datasets.
I have run the cleanup_datasets.py script but I st
Hi all,
When running bwa-mem (installed version 0.7.12.1) I get an empty result with
the stderr giving the following error:
[main] Version: 0.7.12-r1039
[main] CMD: bwa mem -t 1 -v 1 -I 180 localref.fa
/home/galaxy/galaxy/database/files/001/dataset_1958.dat
/home/galaxy/galaxy/database/files/0
o,
> Bjoern
>
> Am 01.03.2016 um 13:39 schrieb C. Ch.:
> > Hi,
> >
> > I've upgraded to 16.01 and have error messages indicating missing
> > modules. This produces problems while setting the metadata. The
> > processes run, the results are there but the h
Hi,
I've upgraded to 16.01 and have error messages indicating missing modules. This
produces problems while setting the metadata. The processes run, the results
are there but the history entry is in red.
How can I trigger the installation of all the modules that galaxy needs with
the new pip bas
olf.h...@fmi.ch
Date: Wed, 10 Jun 2015 11:54:07 +0200
CC: galaxy-dev@lists.galaxyproject.org
To: tuto...@hotmail.com
just double checking:and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. wrote:Hi Hans,
Actually the older dataset h
Date: Wed, 10 Jun 2015 11:54:07 +0200
CC: galaxy-dev@lists.galaxyproject.org
To: tuto...@hotmail.com
just double checking:and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. wrote:Hi Hans,
Actually the older dataset has nothing to do with
2015 10:38:58 +0200
CC: galaxy-dev@lists.galaxyproject.org
To: tuto...@hotmail.com
Hi Cristian
This problem sounds familiar. Have the new and the old file the same name? If
so, try renaming your new gff file.
Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. wrote:Hi all,
I have uploaded a gff
Hi all,
I have uploaded a gff annotation to a shared library and when I try to load it
into trackster it tries consistently to load an older dataset that does not
exist anymore and does not correspond to the real gff dataset file. If I load
the gff into a history, then this file is correctly loa
a general problem you encountered here with unsorted BAM
> files. We can reproduce it locally. Will let you know if I find a
> workaround.
>
> Cheers,
> Bjoer
>
> Am 05.06.2015 um 14:23 schrieb C. Ch.:
> > Hi all, I have a clean local install of galaxy from git (commit:
Hi all,
I have a clean local install of galaxy from git (commit:
40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and I get an
error message (see below) if I do not choose the 'sort' option.I have the
impression that this might be related more to galaxy than to bismark itself.
T
Hi all,
We had a problem on the NAS where we couldn't write anymore. This problem was
solved and I decided that I would profit to upgrade galaxy.
Now we have a problem where jobs do not get launched and the handler log shows
a lot of error messages. The first error message is copied below. Afterw
Hi,
Could this be related to the fact that galaxy is not seeing the tools that are
installed in /usr/local/bin??
I'm on latest_2015.01.13 and since the two last upgrades I saw that
interproscan and bsmap were not found by galaxy. Both are installed in
/usr/local and when invoked on the command
il.com
To: tuto...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org
Ok, found it. This was fixed in revision 14955:5454f62f54df and applied to the
stable branch in 14968:cb0c2ea402e4, and an update should fix your problem.
-Dannon
On Tue, Dec 9, 2014 at 3:32 PM, C. Ch. wrote:
Hi Dannon,
Sorry, for
revision are you running?
-Dannon
On Tue, Dec 9, 2014 at 3:29 PM, C. Ch. wrote:
Hi all,
I have had the following problem while trying to access the "manage jobs" page.
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_ite
Hi all,
I have had the following problem while trying to access the "manage jobs" page.
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__ app_iter = self.application(environ, sr_checker)File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/p
laxy.util.json"
From: dannon.ba...@gmail.com
To: tuto...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org
Hi Cristian,
What revision of Galaxy are you running? I believe this was fixed a while back.
-Dannon
On Thu, Dec 4, 2014 at 10:14 AM, C. Ch. wrote:
Hi All,
While trying to use t
alaxy.util.json"
From: dannon.ba...@gmail.com
To: tuto...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org
Hi Cristian,
What revision of Galaxy are you running? I believe this was fixed a while back.
-Dannon
On Thu, Dec 4, 2014 at 10:14 AM, C. Ch. wrote:
Hi All,
Whi
Galaxy are you running? I believe this was fixed a while back.
-Dannon
On Thu, Dec 4, 2014 at 10:14 AM, C. Ch. wrote:
Hi All,
While trying to use the data_manager_fetch_genome_all_fasta to create a
reference genome I get the following error: No handlers could be found for
logger "g
Hi All,
While trying to use the data_manager_fetch_genome_all_fasta to create a
reference genome I get the following error: No handlers could be found for
logger "galaxy.util.json"
I'm on the latest version of galaxy.
Any idea what is wrong?
Thanks!Cristian
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